Stephen Rong
@alwaysrong.bsky.social
Marie Skłodowska-Curie Actions postdoc in Spivakov Lab at Imperial College. Formerly postdoc at in Reilly Lab at Yale University. The sounds of noncoding variants wake me from my slumber.
Reposted by Stephen Rong
Population genetics simulations and analysis of experimental datasets in yeast, Drosophila and E. coli show that beneficial mutations are abundant but transient, as they become deleterious after environmental turnover (antagonistic pleiotropy)🧪 www.nature.com/articles/s41...
Adaptive tracking with antagonistic pleiotropy results in seemingly neutral molecular evolution - Nature Ecology & Evolution
Population genetics simulations and analysis of experimental datasets in yeast, Drosophila and E. coli show that beneficial mutations are abundant but transient, as they become deleterious after envir...
www.nature.com
November 20, 2025 at 4:31 PM
Population genetics simulations and analysis of experimental datasets in yeast, Drosophila and E. coli show that beneficial mutations are abundant but transient, as they become deleterious after environmental turnover (antagonistic pleiotropy)🧪 www.nature.com/articles/s41...
Reposted by Stephen Rong
My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up!
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
November 20, 2025 at 2:02 PM
My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up!
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.
Check it out!
academic.oup.com/bioinformati...
Reposted by Stephen Rong
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
www.biorxiv.org
November 19, 2025 at 8:57 PM
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Reposted by Stephen Rong
Check out our newest work! This is a story on how to get selectivity in binders - both isoform and site selectivity. Read the paper or enjoy this brief Skytorial of what we did!
www.biorxiv.org/content/10.1...
1/n
www.biorxiv.org/content/10.1...
1/n
PANCS-spec-Binders: A system for rapidly discovering isoform- or epitope-specific binders
Proteins that bind to a target protein of interest, termed "binders," are essential components of biological research reagents and therapeutics. Target proteins present multiple binding surfaces with ...
www.biorxiv.org
November 19, 2025 at 6:10 PM
Check out our newest work! This is a story on how to get selectivity in binders - both isoform and site selectivity. Read the paper or enjoy this brief Skytorial of what we did!
www.biorxiv.org/content/10.1...
1/n
www.biorxiv.org/content/10.1...
1/n
Reposted by Stephen Rong
Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.
Apply by Dec 15th here: shorturl.at/4a4O6
Apply by Dec 15th here: shorturl.at/4a4O6
Early Career Scientist Awards 2026
Application to the UW-Madison Evolution Seminar Series - Early Career Scientist Awards.
urldefense.com
November 19, 2025 at 8:55 PM
Wisconsin Evolution is accepting applications for our Seminar Series' Early Career Scientist Award. Come share your evolution research and visit UW-Madison's evolution community. Open to grad students and postdocs (<5 yrs post PhD) from outside UW-Madison.
Apply by Dec 15th here: shorturl.at/4a4O6
Apply by Dec 15th here: shorturl.at/4a4O6
Reposted by Stephen Rong
@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪
www.nature.com/articles/d41...
www.nature.com/articles/d41...
How do genetic association studies rank genes?
Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.
www.nature.com
November 19, 2025 at 6:43 PM
@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Stephen Rong
We are looking for a postdoctoral fellow to work on induced proximity 🤜🤛 and functional genomics! Join our team in Toronto 🇨🇦 to tackle major challenges in oncology and neurodegeneration. www.nature.com/naturecareer...
POSTDOCTORAL FELLOW - Toronto (City), Ontario (CA) job with Taipale Lab, Donnelly Centre, University of Toronto | 12849004
The Taipale lab in the Donnelly CCBR and University of Toronto is looking for a highly motivated Postdoctoral Fellow
www.nature.com
November 19, 2025 at 5:51 PM
We are looking for a postdoctoral fellow to work on induced proximity 🤜🤛 and functional genomics! Join our team in Toronto 🇨🇦 to tackle major challenges in oncology and neurodegeneration. www.nature.com/naturecareer...
Reposted by Stephen Rong
Connect with the UK’s #bioinformatics and #computationalbiology community at #ISCBUK 2026. Share your latest research, build new collaborations, and be part of this inaugural meeting.
Submissions are open until February 5, 2026.
📥 Submit: https://www.iscb.org/uk2026/call-for-submissions/abstracts
Submissions are open until February 5, 2026.
📥 Submit: https://www.iscb.org/uk2026/call-for-submissions/abstracts
November 19, 2025 at 11:16 AM
Connect with the UK’s #bioinformatics and #computationalbiology community at #ISCBUK 2026. Share your latest research, build new collaborations, and be part of this inaugural meeting.
Submissions are open until February 5, 2026.
📥 Submit: https://www.iscb.org/uk2026/call-for-submissions/abstracts
Submissions are open until February 5, 2026.
📥 Submit: https://www.iscb.org/uk2026/call-for-submissions/abstracts
Reposted by Stephen Rong
I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new...
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Why we made Affinity free, and how we’ll keep it that way
We’ve made Affinity completely free, empowering professional designers with studio-grade creative software, supported by Canva’s sustainable ecosystem.
www.canva.com
November 18, 2025 at 11:28 PM
I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new...
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Reposted by Stephen Rong
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
A Grammar of Graphics for Comparative Genomics
An extension of ggplot2 for creating complex genomic maps. It builds on the power of ggplot2 and tidyverse adding new ggplot2-style geoms & positions and dplyr-style verbs to manipulate the…
thackl.github.io
November 18, 2025 at 7:02 PM
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
Reposted by Stephen Rong
🦣🧬🦣🤯💥We are pleased to share our new paper about ancient RNA expression profiles from the Woolly Mammoth, now published in Cell @cellpress.bsky.social
www.cell.com/cell/fulltex...
If you want to know more, read the 🧵 below:
www.cell.com/cell/fulltex...
If you want to know more, read the 🧵 below:
November 14, 2025 at 4:08 PM
🦣🧬🦣🤯💥We are pleased to share our new paper about ancient RNA expression profiles from the Woolly Mammoth, now published in Cell @cellpress.bsky.social
www.cell.com/cell/fulltex...
If you want to know more, read the 🧵 below:
www.cell.com/cell/fulltex...
If you want to know more, read the 🧵 below:
Reposted by Stephen Rong
This study is WILD - some dinosaurs (reptiles) had hooves, and this is now the earliest known fossil of a hooved animal. Even crazier, mammals may have secondarily LOST their hooves through evolutionary adaptations (the origin of hooves is still kinda murky) www.science.org/doi/10.1126/...
November 16, 2025 at 3:25 PM
This study is WILD - some dinosaurs (reptiles) had hooves, and this is now the earliest known fossil of a hooved animal. Even crazier, mammals may have secondarily LOST their hooves through evolutionary adaptations (the origin of hooves is still kinda murky) www.science.org/doi/10.1126/...
Reposted by Stephen Rong
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
November 13, 2025 at 8:34 PM
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Reposted by Stephen Rong
"What James Watson got wrong about DNA"
By the great Sohini Ramachandran (@sramach.bsky.social) and your boy for The Boston Globe (@bostonglobe.com).
www.bostonglobe.com/2025/11/14/o...
By the great Sohini Ramachandran (@sramach.bsky.social) and your boy for The Boston Globe (@bostonglobe.com).
www.bostonglobe.com/2025/11/14/o...
What James Watson got wrong about DNA - The Boston Globe
The science he helped pioneer consistently undermines his view that genes determine everything about us.
www.bostonglobe.com
November 14, 2025 at 4:50 PM
"What James Watson got wrong about DNA"
By the great Sohini Ramachandran (@sramach.bsky.social) and your boy for The Boston Globe (@bostonglobe.com).
www.bostonglobe.com/2025/11/14/o...
By the great Sohini Ramachandran (@sramach.bsky.social) and your boy for The Boston Globe (@bostonglobe.com).
www.bostonglobe.com/2025/11/14/o...
Reposted by Stephen Rong
Multimodal learning enables chat-based exploration of single-cell data www.nature.com/articles/s41... 🧬🖥️🧪 github.com/epigen/cellw...
November 14, 2025 at 7:01 PM
Multimodal learning enables chat-based exploration of single-cell data www.nature.com/articles/s41... 🧬🖥️🧪 github.com/epigen/cellw...
Reposted by Stephen Rong
SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the
@simonsfoundation.org. Details to follow. Please RT.
@simonsfoundation.org. Details to follow. Please RT.
November 14, 2025 at 5:05 PM
SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the
@simonsfoundation.org. Details to follow. Please RT.
@simonsfoundation.org. Details to follow. Please RT.
Reposted by Stephen Rong
Which human brain circuits are implicated in neurodevelopmental conditions? We bridged human genetics, spatial transcriptomics and neurodevelopment to discover the convergence of autism-associated genes in the developing human thalamus! www.biorxiv.org/content/10.1...
November 11, 2025 at 10:55 AM
Which human brain circuits are implicated in neurodevelopmental conditions? We bridged human genetics, spatial transcriptomics and neurodevelopment to discover the convergence of autism-associated genes in the developing human thalamus! www.biorxiv.org/content/10.1...
Reposted by Stephen Rong
Interesting, from @garvaninstitute.bsky.social.
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
Impact of Rare and Common Genetic Variation on Cell Type-Specific Gene Expression
Understanding the genetic basis of gene expression can shed light on the regulatory mechanisms underlying complex traits and diseases. Single cell-resolved measures of RNA levels and single-cell expre...
www.medrxiv.org
November 12, 2025 at 3:15 PM
Interesting, from @garvaninstitute.bsky.social.
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
Reposted by Stephen Rong
Come and join us here in Cambridge! Applications open for a new faculty position, for a researcher in computational and/or theoretical biology, based jointly in Genetics and Mathematics. Happy to answer questions about research, teaching and working here.
www.cam.ac.uk/jobs/faculty...
www.cam.ac.uk/jobs/faculty...
Faculty Position in Computational Biology
Applications are invited for an Assistant/ Associate Professorship in Computational Biology to commence on 1 April 2026 or shortly thereafter. This is a joint post between the Department of Applied
www.cam.ac.uk
November 11, 2025 at 9:05 PM
Come and join us here in Cambridge! Applications open for a new faculty position, for a researcher in computational and/or theoretical biology, based jointly in Genetics and Mathematics. Happy to answer questions about research, teaching and working here.
www.cam.ac.uk/jobs/faculty...
www.cam.ac.uk/jobs/faculty...
Reposted by Stephen Rong
SYNTH is a radical departure from the classic pre-training recipe: what if we trained for reasoning and focused on the assimilation of knowledge and skill that matters? At its core it’s an upsampling of Wikipedia 50,000 “vital” articles. huggingface.co/datasets/Ple...
November 10, 2025 at 5:30 PM
SYNTH is a radical departure from the classic pre-training recipe: what if we trained for reasoning and focused on the assimilation of knowledge and skill that matters? At its core it’s an upsampling of Wikipedia 50,000 “vital” articles. huggingface.co/datasets/Ple...
Reposted by Stephen Rong
Excited to share Nona: a unifying multimodal masking framework for functional genomics.
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
November 10, 2025 at 9:01 PM
Excited to share Nona: a unifying multimodal masking framework for functional genomics.
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).
Can these be unified under a single paradigm? 1/15
Reposted by Stephen Rong
📣 Paper alert!
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
November 10, 2025 at 11:11 AM
📣 Paper alert!
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today!
journals.biologists.com/dev/article/...
Reposted by Stephen Rong
A meta-analysis of the impact of polygenic risk score disclosures on health outcomes. 27 RCTs, max follow up 12 months.
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
Effects of polygenic risk score communication on health outcomes: systematic review and meta-analysis
Abstract Objective. The purpose of this systematic review and meta-analysis is to summarize evidence from all RCTs to-date on the efficacy of polygenic risk score (PRS) communication in changing healt...
www.medrxiv.org
November 7, 2025 at 8:33 AM
A meta-analysis of the impact of polygenic risk score disclosures on health outcomes. 27 RCTs, max follow up 12 months.
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
For 22 outcomes tested in >=2 trials,
"Meta-analysis revealed no statistically significant effects on any measured outcome"
www.medrxiv.org/content/10.1...
Reposted by Stephen Rong
BehaveAI is live!
Our biologically inspired video analysis tool sees motion as colour. Track animals or objects, classify their behaviour, and handle complex natural scenes with ease.
Semi-supervised annotation, no GPUs required, user-friendly, free & open source.
Pre-print tinyurl.com/BehaveAI
Our biologically inspired video analysis tool sees motion as colour. Track animals or objects, classify their behaviour, and handle complex natural scenes with ease.
Semi-supervised annotation, no GPUs required, user-friendly, free & open source.
Pre-print tinyurl.com/BehaveAI
November 6, 2025 at 10:09 AM
BehaveAI is live!
Our biologically inspired video analysis tool sees motion as colour. Track animals or objects, classify their behaviour, and handle complex natural scenes with ease.
Semi-supervised annotation, no GPUs required, user-friendly, free & open source.
Pre-print tinyurl.com/BehaveAI
Our biologically inspired video analysis tool sees motion as colour. Track animals or objects, classify their behaviour, and handle complex natural scenes with ease.
Semi-supervised annotation, no GPUs required, user-friendly, free & open source.
Pre-print tinyurl.com/BehaveAI
Reposted by Stephen Rong
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...